Fix motion correction and CNMF for 3D movies

ethanbb commented 2 months ago

The mcorr algorithm currently fails when run on a 3D movie during correlation image calculation. This is due to some code in caiman that could probably also be changed to get it to work (flatironinstitute/caiman#1363 does half of it), but this PR should fix mcorr in a way that is also compatible with existing caiman versions:

By passing the file in as a string rather than list, load_file_chain does not get called, which means is3D is not needed (otherwise this throws an error).
I added a try/catch that should catch the specific bug fixed in flatironinstitute/caiman#1363 and tries again without baseline removal to avoid it.

This PR is dependent on #298 (to avoid an ugly merge) so I'm submitting it as a draft for now. Also, it would be good to add a test case for 3D motion correction (with test data and everything). But at least the current tests pass (except for the 2 that are always failing) so it doesn't break 2D mcorr.

kushalkolar commented 2 months ago

rebase this on main once #298 is merged

kushalkolar commented 1 month ago

wait until next release of caiman and then pin the next release of mescore to that

ethanbb commented 1 month ago

Caiman PR is merged, but still waiting for next release to mark as ready for review.

ethanbb commented 1 month ago

Caiman 1.11.2 is released

kushalkolar commented 2 weeks ago

Lgtm!

nel-lab / mesmerize-core

Fix motion correction and CNMF for 3D movies #300